Whereas many independent methods are used to estimate snow water equivalent (SWE) and its spatial distribution and seasonal variability, a need exists for a systematic characterization of inter-model differences at annual, seasonal, and regional scales necessary to quantify the associated uncertainty in these datasets. This study conducts a multi-scale validation and comparison, based on Airborne Snow Observatory data, of five state-of-the-art SWE datasets in the Sierra Nevada, California, including three SWE datasets from retrospective models: an INiTial REConstruction model (REC-INT), an improved REConstruction model based on the ParBal energy balance model (REC-ParBal), and a Sierra Nevada SWE REConstruction with Data Assimilation (REC-DA), and two operational SWE datasets from the U.S. National Weather Service, including the Snow Data Assimilation System (SNODAS) and the National Water Model (NWM-SWE). The results show that REC-DA and REC-ParBal provide the two most accurate estimates of SWE in the snowmelt season, both with small positive biases. REC-DA provides the most accurate spatial distribution of SWE (R2 = 0.87, MAE = 66 mm, PBIAS = 8.3%) at the pixel scale, while REC-ParBal has the least basin-wide PBIAS (R2 = 0.79, MAE = 73 mm, PBIAS = 4.1%) in the snowmelt season. Moreover, REC-DA underestimates peak SWE by −5.8%, while REC-ParBal overestimates it by 7.5%, when compared with the measured peak SWE at snow pillow stations across the Sierra Nevada. The two operational SWE products—SNODAS and NWM-SWE—are less accurate. Furthermore, the inter-model comparison reveals a certain amount of disagreement in snow water storage across time and space between SWE datasets. This study advances our understanding of regional SWE uncertainties and provides critical insights to support future applications of these SWE data products and therefore has broad implications for water resources management and hydrological process studies.